The plots viewed from the screen are the results of the optimization process. The program goes through a dozen or more iterations of each part of the trajectory before arriving at the best fit. The exact data used for these optimized flight paths are accessible via the editable Data forms. The Figures give a general idea of how this optimization is done. Some comments on the graphs:
One dot is plotted for each time step. The variable step integrator takes the largest possible step for the most accurate trajectory. The closer the spacecraft gets to a major body, the more steps are taken to model the forces. An artificial constraint is placed on the calculations, using a fixed step, when approaching the Sphere of Influence. This is so that the transfer of coordinates can be done as close to the real SOI as possible.
A spline curve is fit to the data points when the graph is a solid line instead of dots. This is done to give you a sense of the complete trajectory.
All the plots are created using equal units on the x- and y-axes. If you drag the screen to be a rectangle, this may distort the figure.
The colored circle at the origin in planet centered coordinate plots is the size of the planet itself, to give some perspective. The axes are scaled to the exact dimensions of the Sphere of Influence of the respective planet.
A yellow Hohmann Transfer with the geometry of the two-body ellipse is drawn for comparison on the heliocentric graphs. This is the "nominal trajectory." The spacecraft always starts exactly on this ellipse, since that's how the initial conditions are determined. With no external thrusts applied, and no optimization parameters selected, the spacecraft follows this path quite closely.
A complete hyperbola is drawn in the large scale Planet flyby plots to give you a sense of the geometry of a gravity assist. The actual trajectory of the spacecraft is stopped at the planet, as indicated in the text report.